step08_first_level_analysis.sh

#!/bin/bash
#-----------------------------------------------------------
# The script will run the first_level_script.py script for each subject.
#
# You will need a conda environment that contains the required packages.
#
# Usage:
#   Configure the variables below and run the script: ./step08_first_level_analysis.sh
#-----------------------------------------------------------

# ------------------------------------------------------------
#
# !FILL IN THE VARIABLES BELOW!
#
# ------------------------------------------------------------
# Your project's root directory
PROJECT_PATH='/imaging/correia/da05/workshops/2024-CBU'

# Location of the first-level python script
SCRIPT_PATH="$PROJECT_PATH"/code/first_level_script.py

# Path to the job logs
JOB_DIR="$PROJECT_PATH"/work/first-level_job_logs

# Which conda environment to use
CONDA_ENV=fmri

# ------------------------------------------------------------
#
# You don't have to change anything below this line!
#
# ------------------------------------------------------------

# ----------------------------------------------------------
# Get the subject list 
# ----------------------------------------------------------
SUBJECT_DIRS=("$PROJECT_PATH"/data/sub-*)
SUBJECT_LIST=("${SUBJECT_DIRS[@]##*/}") 
# ----------------------------------------------------------

# CD to the job logs directory
mkdir -p "$JOB_DIR"
cd "$JOB_DIR" || exit

# ----------------------------------------------------------
# Do some checks before submitting the job
# ----------------------------------------------------------
echo "Checking if the project directory exists..."
if [ ! -d "$PROJECT_PATH" ]; then
    echo "Project directory does not exist: $PROJECT_PATH"
    exit 1
fi

echo "Checking if the first-level python script exists..."
# Check if the script exists
if [ ! -f "$SCRIPT_PATH" ]; then
    echo "The script $SCRIPT_PATH does not exist"
    exit
fi

echo "Checking if the conda environment exists..."
if ! conda env list | grep -q "$CONDA_ENV"; then
    echo "The conda environment $CONDA_ENV does not exist"
    exit
fi

#-----------------------------------------------------------
# Activate the environment and submit job for each subject
#-----------------------------------------------------------
conda activate "$CONDA_ENV"

# Couldn't use task array because passing a list as an argument is tricky.
# For loop is fine too.
for sub in "${SUBJECT_LIST[@]}"; do
     sbatch \
        --job-name=first_level \
        --cpus-per-task=16 \
        "$SCRIPT_PATH" "${PROJECT_PATH}" "${sub}"
done

conda deactivate